Inflammatory Bowel Diseases (IBDs), namely ulcerative colitis (UC) and Crohn's disease (CD), are chronic, lifelong, relapsing illnesses, affecting close to 1 million Americans and costing approximately 2 billion dollars/year to the US healthcare system. IBDs are of unknown cause, have no cure and are increasing in incidence. We have found that the diversity of the mucosa associated or luminal wall adherent microbial populations is decreased in IBD. We also identified putative peaks in LH-PCR fingerprints that may indicate patterns associated with IBD. Furthermore, linkage of our LH-PCR fingerprints to clone sequences show that certain bacterial groups are present in the mucosal flora of IBD patients. These findings have led us to hypothesize that there is a protective biofilm of bacteria adhering to the Ileocolonic wall and an invasion of this protective biofilm by lumen bacteria in IBD (dysbiosis). Our initial results indicate that there is little variation in this protective biofilm along the colon and ileum. Our initial observations also indicate that the lumen/stool microflora may be indicative of the disease state. Our goal is to determine the feasibility of monitoring dysbiosis by fingerprinting rectal swabs and stool samples collected by the patient. Our second aim is to fully characterize these microflora communities by pyrosequencing mucosal, lumen, rectal swab, and stool samples. If we demonstrate that stool cards and rectal swabs are a reliable representation of the lumen and mucosal bacterial patterns, then our diagnostic test will be the most feasible, noninvasive and easy test to assess dysbiosis. Patients can place their stool on the cards (or physicians can place the stool on the card after rectal examination) and mail them to our central laboratory for bacterial fingerprinting. The goal is to identify flare up before it becomes clinically apparent and thus prevent the symptomatic flare-ups with damage to the intestinal track. This could clearly improve quality of life and prevent the complication of surgery. Studies that characterize microflora in humans using powerful techniques from environmental microbiology can bring about significant advances in the understanding of these illnesses. There is a growing recognition of the importance of microflora in health and disease not limited to IBD but also in other areas such as colorectal carcinogenesis, intestinal infections, celiac disease, irritable bowel syndrome, prebiotic and probiotic therapies. This proposal involves the first time use of a sophisticated and highly reproducible bacterial fingerprinting tool, LH-PCR, in the study of microflora in the GI tract. The team assembled for this proposal is interdisciplinary and combines three very valuable sets of expertise to address the complexity of the GI microflora, namely clinical IBD expertise, environmental microbiology expertise, and bioinformatics expertise to analyze complex sets of data. New diagnostic tools based on LH-PCR can be utilized for routine real-time clinical use as direct result of this proposal. Such a tool can then be used to help determine the absence/presence of disease; and predict the various phenotypic presentations of the disease, the disease course, and treatment effects. If distinct differences between the microflora of controls and IBD are defined as proposed, it would be also feasible to implement a clinical diagnostic for IBD with major commercial potential. If we demonstrate that stool card is a reliable representation of the mucosal attached bacterial pattern and rectal swabs are a surrogate for mucosal biopsies, then our diagnostic test will be the most feasible, noninvasive and easy test to assess dysbiosis. Patients can place their stool on the cards (or physicians can place the stool on the card after rectal examination) and mail them to our central laboratory for bacterial fingerprinting. Furthermore, patients (or primary care physicians) can safely insert the swab in the rectum and rub it against the rectal mucosa and obtain the sample and then send it to our central laboratory for bacterial fingerprinting. [unreadable] [unreadable] [unreadable]